Where do I annotate my military retirement 1099-R. I have already been working on my W-2 from my employer.

Yes, you will need to enter your 1099-R for your military retirement. This is how to do that in TurboTax:

1. Select Federal, then  Wages & Income.
2. Find IRA, 401(k), Pension Plan Withdrawals (1099-R) under Retirement Plans and Social Security, select Start to the right.
3. Answer Yes on the next screen, or if you already have an entry in this section, click Add another 1099-R at the bottom of the screen.
4. Click Continue.
5. Follow the steps to import your 1099-R, or scroll to the bottom and select Change how I enter my form.
6. On the next screen select, I'll type it in myself.
7. On the next screen select Financial institution or other provider (1099-R)
   and click Continue.
8. Fill in the next screens with the figures from your form. 
9. On the screen, Where is your distribution from? check the box next to Retired or retainer pay of the uniformed services of the U.S.
10. Continue until you finish this section.